Therefore, different methods of annotation (e.g., whether or not all ORFs are annotated) lead to ambiguities.
However, if this is not coupled with high-throughput methods of annotation, we are diminishing its real potential.
The large numbers of protein sequences generated by whole genome sequencing projects require rapid and accurate methods of annotation.
Two methods of annotation have been adopted manually using web based data entry tool and data imported electronically through XML files [ 27].
Out of 331 different CAZy enzyme families, 243 were found in both soil samples (WS-72 and GL-72) at least through one of the three methods of annotation (CAT, MG-RAST and blastx) (Supplementary Table S5).
Besides the common problem of missing short genes, it was difficult to determine the reasons for missing the longer genes, as the methods of annotation were not always detailed in GenBank or in the annotations' associated publications.
Although there are almost certainly genes that we did not find as part of this study, we believed that by focusing attention on these unannotated genes and the reasons for their absence, we can bring attention to the many various methods of annotation currently in use and the need for standardization.
In this section, we present the experimental setup to acquire the test dataset, methods of data annotation, analysis of attention levels as observed by annotators, and their correspondence to student behavior.
Comparative analysis was performed using a second set of rice genome annotation data, from the RAP (http://rapdb.dna.affrc.go.jp), to evaluate the effect of different methods of genome annotation on our results.
